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GCA_000648525.1 | [
"CP007586.1"
] | [["AHY14923.1","AHY14924.1","AHY14925.1","AHY14926.1","AHY14927.1","AHY14928.1","AHY14929.1","AHY149(...TRUNCATED) | [["MTENEQIFWNRVLELAQNQLTQATYEFFVFDARLVKVENQVATIYLESVKQLFWENNLKDVILTAGFEIYNAQISIEYVFEDYLEESQPAQSNTQVF(...TRUNCATED) | 1346 | [[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,nul(...TRUNCATED) | [[118,1629,2827,3253,4439,5011,8474,10014,10273,10781,12064,13352,13916,16239,17574,18124,18939,2024(...TRUNCATED) | [[1473,2765,3024,4371,5008,8511,9985,10286,10644,12067,13347,13894,15883,17381,18089,18903,19229,216(...TRUNCATED) | [["chromosomal replication initiator protein DnaA","DNA polymerase III subunit beta","hypothetical p(...TRUNCATED) | 0 |
GCF_034258515.1 | [
"NZ_CP139438.1"
] | [["WP_157240151.1","WP_321214845.1","WP_321214846.1","WP_321214847.1","WP_157240147.1","WP_321214848(...TRUNCATED) | [["MTVDEANHANTVGSSWRRVVSLLEQDHRVSPRQRGFVILAQAQGLIGSTLLVAVPNELTREVLQTQVKDALDDALHNVFSEDIRCAIDVDTDLVPIH(...TRUNCATED) | 1671 | [["dnaA","dnaN","gnd","recF",null,"gyrB","gyrA",null,null,null,null,null,null,null,null,null,null,nu(...TRUNCATED) | [[1,1951,3194,4125,5320,6260,8405,11076,11983,12344,13314,14328,15424,15979,17387,18037,18722,19148,(...TRUNCATED) | [[1425,3075,4078,5336,5880,8347,11083,11744,12099,13294,14189,15269,15969,16857,17854,18651,18973,19(...TRUNCATED) | [["chromosomal replication initiator protein DnaA","DNA polymerase III subunit beta","phosphoglucona(...TRUNCATED) | 1 |
GCF_000315445.1 | ["NZ_JH992957.1","NZ_JH992958.1","NZ_JH992959.1","NZ_JH992960.1","NZ_JH992961.1","NZ_JH992962.1","NZ(...TRUNCATED) | [["WP_003776039.1","WP_003776042.1","WP_003776045.1","WP_003776047.1","WP_003776049.1","WP_003776051(...TRUNCATED) | [["MKERKLFTSESVSEGHPDKVADQISDAILDALLAQDSQSRVACEVTVNTGLVLITGEIRTTAYVDMAQVVRETLKDIGYTRAKYGFDADNVAVLVSI(...TRUNCATED) | 883081 | [["metK",null,null,null,"pgsA",null,"recA","rny",null,null,null,null,null,null,"mutS","mutL","msrB",(...TRUNCATED) | [[2988,4204,5448,6807,7468,8241,9532,10858,12666,13717,13869,14426,15295,18106,18922,21534,23519,239(...TRUNCATED) | [[4187,5451,6734,7418,8049,9440,10602,12417,13736,13908,14420,15163,16803,18906,21519,23507,23950,25(...TRUNCATED) | [["methionine adenosyltransferase","pitrilysin family protein","pitrilysin family protein","helix-tu(...TRUNCATED) | 1 |
GCF_900187305.1 | [
"NZ_LT906434.1"
] | [["WP_085363466.1","WP_169835319.1","WP_085363464.1","WP_085363463.1","WP_157739130.1","WP_085363462(...TRUNCATED) | [["MLILQAERDALLKPLQAVTGIVERRHTLPILSNVLLENLHGQTNILATDLEIQINTSGPHSEAEDFRITTNAKKLQDILRALPDGSLIALDWAQNRL(...TRUNCATED) | 326523 | [["dnaN",null,null,"aroG",null,"pgi",null,null,null,null,null,"pncC",null,null,null,"miaB",null,"ycc(...TRUNCATED) | [[1517,2683,5134,7373,8483,8847,10747,12269,13082,13670,14648,16059,17054,17773,19522,19924,21489,22(...TRUNCATED) | [[2620,5085,7302,8416,8629,10484,12189,13060,13543,14497,15544,16535,17662,19245,19902,21243,21983,2(...TRUNCATED) | [["DNA polymerase III subunit beta","TPR end-of-group domain-containing protein","primosomal protein(...TRUNCATED) | 1 |
GCF_004102925.1 | [
"NZ_CP035093.1"
] | [["WP_128718700.1","WP_128718701.1","WP_003166006.1","WP_003166007.1","WP_003166008.1","WP_003166009(...TRUNCATED) | [["MKIAILGAGVIGVTTAHYLARQGHEVTVIDRQTGPALETSFANAGEISPGYSSPWAAPGIPAKAVKWLFMRHAPLILHPQINAPTVRWLLALLRNCT(...TRUNCATED) | 293 | [[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,nul(...TRUNCATED) | [[437,1725,2174,2765,3141,3683,4081,5115,5978,6468,8807,9169,9450,11494,12625,13872,14554,16151,1793(...TRUNCATED) | [[1693,2177,2761,3139,3686,4072,5118,5981,6463,8780,9172,9450,11429,12216,13875,14477,15999,17821,21(...TRUNCATED) | [["D-amino acid dehydrogenase","chemotaxis protein CheE","response regulator","hypothetical protein"(...TRUNCATED) | 1 |
GCF_000025805.1 | [
"NC_014103.1"
] | [["WP_013081315.1","WP_013054821.1","WP_013054822.1","WP_013054823.1","WP_013081316.1","WP_013081317(...TRUNCATED) | [["MENIHDLWNRALDQIEKKLSKPSFETWLKSTKAHALQGDTLIITAPNDFARDWLESRYSNLIAETLYDLTGEELDVKFIIPPNQAEEEFDIQAPKKK(...TRUNCATED) | 592022 | [["dnaA","dnaN","yaaA","recF","gyrB","gyrA",null,"guaB",null,"pdxS","pdxT","serS",null,null,null,nul(...TRUNCATED) | [[1,1532,2769,2999,4358,6401,14261,15343,16959,18505,19414,20324,21927,22607,23386,24744,25366,26334(...TRUNCATED) | [[1344,2668,2984,4117,6274,8911,15226,16809,18314,19392,20001,21601,22607,23242,24687,25286,25836,28(...TRUNCATED) | [["chromosomal replication initiator protein DnaA","DNA polymerase III subunit beta","S4 domain-cont(...TRUNCATED) | 1 |
GCF_001642655.1 | [
"NZ_CP014170.1",
"NZ_CP014171.1"
] | [["WP_017751997.1","WP_017895888.1","WP_017751995.1","WP_017751994.1","WP_017751993.1","WP_017895889(...TRUNCATED) | [["MNAYLKELWDKTLNIIKGELTEVSFNTWLKSITPISIEDNVLKLSVPNELTRGVLDNKYKEYIIKALKILTSKNYTIEFSIYQEEAFTLDEKDTQHR(...TRUNCATED) | 1519 | [["dnaA","dnaN",null,"recF",null,"gyrB","gyrA",null,null,null,null,null,"serS",null,null,null,null,n(...TRUNCATED) | [[234,1833,2964,3234,4347,4629,6561,14603,15203,15767,18643,20061,20640,22115,22804,24102,24843,2528(...TRUNCATED) | [[1574,2936,3170,4325,4610,6542,9002,15097,15718,18490,20037,20342,21920,22714,23376,24656,25229,257(...TRUNCATED) | [["chromosomal replication initiator protein DnaA","DNA polymerase III subunit beta","RNA-binding S4(...TRUNCATED) | 0 |
GCF_025150745.1 | [
"NZ_CP102282.1"
] | [["WP_005362325.1","WP_005362327.1","WP_005362330.1","WP_005362333.1","WP_005362336.1","WP_005362338(...TRUNCATED) | [["MTDFLTADTNLPSYMMFPRFLLNMEINETAKMLYIILLDRARLSQKNEGWSDIAGHVFIYFTIEALAEVLHKSQMTVKTALAVLEKQELIFRKRQGP(...TRUNCATED) | 39496 | [[null,null,null,"mobQ",null,null,null,null,null,"rlmD",null,"pcrA",null,null,null,null,"hslO",null,(...TRUNCATED) | [[1,714,1742,2101,3871,6434,7213,8118,8934,9337,11089,11410,14045,14990,15664,17002,17361,18319,1924(...TRUNCATED) | [[717,1571,1963,3810,6420,7114,8121,8801,9305,10986,11325,13743,14644,15655,16839,17298,18233,19077,(...TRUNCATED) | [["replication initiator protein A","ATP-binding protein","DUF3847 domain-containing protein","MobQ (...TRUNCATED) | 0 |
GCF_000286275.1 | [
"NC_018405.1"
] | [["WP_014881867.1","WP_014881868.1","WP_014881869.1","WP_014881870.1","WP_014881871.1","WP_014881872(...TRUNCATED) | [["MPLSAQQLAAQKNLSYVLAEKLAQRILAGKYAPGSILPGEMELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQELLSWWMTE(...TRUNCATED) | 208224 | [[null,"mdtD","rbsR","rbsK","rbsB","rbsC","rbsA","rbsD","kup","ravA","viaA","asnA","asnC","mioC","mn(...TRUNCATED) | [[153,857,2256,3252,4288,5206,6176,7689,8335,10426,11916,13368,14512,15061,15885,17882,19125,19514,2(...TRUNCATED) | [[860,2290,3248,4181,5178,6171,7681,8108,10203,11922,13367,14360,14970,15510,17774,18508,19505,20329(...TRUNCATED) | [["FadR/GntR family transcriptional regulator","multidrug transporter subunit MdtD","ribose operon t(...TRUNCATED) | 1 |
GCF_006742345.1 | [
"NZ_AP019724.1",
"NZ_AP019725.1",
"NZ_AP019726.1",
"NZ_AP019727.1",
"NZ_AP019728.1"
] | [["WP_005827286.1","WP_141981163.1","WP_009037933.1","WP_141981166.1","WP_005830212.1","WP_005830204(...TRUNCATED) | [["MSEIDHVGLWNRCLEIIRDNVPEQTYKTWFLPIIPLKYEDKTLVVQVPSQFFYEFLEDKFVDLLRKTLYKVIGEGTKLMYNVMVDKSSRKTVDLEST(...TRUNCATED) | 820 | [["dnaA",null,null,null,"folB",null,null,null,"mtaB",null,null,null,"rplI","rpsR","rpsF",null,null,n(...TRUNCATED) | [[1,1458,2610,5279,8247,9266,9832,10841,11795,13197,15028,15574,16096,16561,16836,17340,17987,18253,(...TRUNCATED) | [[1386,2192,5147,7972,8612,9784,10848,11740,13111,14870,15240,15819,16545,16833,17180,17786,18163,18(...TRUNCATED) | [["chromosomal replication initiator protein DnaA","NADPH-dependent oxidoreductase","adenosylcobalam(...TRUNCATED) | 0 |
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in Data Studio
Dataset for predicting Catalase phenotype from whole bacterial genomes (protein sequences)
A dataset of over 1k bacterial genomes across species with the Catalase as label. Catalase denotes whether a bacterium produces the catalase enzyme that breaks down hydrogen peroxide (H₂O₂) into water and oxygen, thereby protecting the cell from oxidative stress. Here, we provide binary Catalase labels, therefore the problem is a binary classification problem.
The genome protein sequences have been extracted from GenBank. Each row contains a list of protein sequences present in the bacterial genome, ordered by their location on the chromosome and plasmids.
The phenotypic traits have been extracted from [1].
Usage
Please see the Finetuning Bacformer for phenotypic traits prediction tutorial for an example on how to use the dataset.
References
[1] Weimann, Aaron, et al. "From genomes to phenotypes: Traitar, the microbial trait analyzer." MSystems 1.6 (2016): 10-1128.
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